Ideas
I have this issue also. I've had both cows and llamas stuck in the household inventory and personal inventory of the sim (after fairs and moves). I cannot put them back into the barns. I also noticed the barns will randomly become filthy like an animal occupies it, but there's no animal inside. Grim will also show up at the barn waiting to reap an animal that never comes out. He's just stuck there with no option to interact apart from the grayed out warning not to try to interact with him before a reaping has taken place, lest you be reaped.
I have no mods and first noticed the issue after purchasing the horse ranch expansion. I have since also purchased the For Rent and Life and Death packs. The issue remains the same through those purchases.